An apparatus and method for manufacturing a flexible display device by a roll-to-roll method, are discussed. According to an embodiment, the apparatus includes a substrate transferring part for transferring a lower substrate attached onto a carrier substrate; a substrate separating part for separating the carrier substrate from the lower substrate transferred by the substrate transferring part; an upper bonding part for bonding an upper substrate to an upper surface of the lower substrate from which the carrier substrate is separated; and a lower bonding part for bonding a rear substrate to a lower surface of the lower substrate from which the carrier substrate is separated.